This document discusses several topics related to chemistry and biochemistry. It covers (1) the basics of thermodynamics and how it relates to chemical reactions, (2) the properties of gases, (3) factors that influence the rate of chemical reactions including temperature, concentration, and catalysts, and (4) optimization of enzyme assays including minimizing background noise and improving precision. It also discusses (5) chemical interactions at enzyme active sites, and (6) hydrophobic interactions in biological molecules.

1. Chemistry for Life
Sciences
Lecture FIVE
A. Mudavanhu

2. Energetics (Thermodynamics)
• the field that studies the energetics of chemical reactions
• The change in enthalpy is usually equal to the amount of heat gained
or lost, so those two are often used interchangeably.
• Thermodynamics can tell us both if a reaction is likely to proceed and
how far it is likel
• A system that is lower in energy is considered more stable.
• A ball at the top of a ramp is higher-energy (less stable), whereas that
ball on the floor is lower-energy (more stable).
• A system will tend to move from higher to lower energy to become
more stable --- the ball will spontaneously roll down the ramp.

3. Energetics (Thermodynamics)
• A reaction energy diagram can summarize the energetics taking place.
• These diagrams show some type of energy on the vertical axis --- higher up
is higher in energy.
• They show reaction progress, or time, on the horizontal axis --- further to
the right means the reaction has gone further, or more time.
• Figure shows a reaction in which the reactants are higher in energy and the
products are lower in energy.
• If looking at energy (E) or enthalpy (H), the reaction would be described as
“exothermic” because it would give off (lose or emit) heat.
• Reactions with negative changes in energy or enthalpy are more likely to be
spontaneous.

4. Energetics (Thermodynamics)

5. The properties of gases
• The molecules that make up a gas are point masses, meaning they have no volume.
• Gas particles are spread out with very great distance between each molecule. Thus, intermolecular forces
are essentially zero, meaning they neither attract nor repel each other.
• If collisions do occur between gas particles, these collisions are elastic, meaning there is no loss of kinetic
(motion) energy.
• Gas molecules are in continuous random motion.
• Temperature is directly proportionate to kinetic energy.

6. Chemical kinetics and enzymes.
• Chemical kinetics is the study of chemical reactions with respect to
the rate of reaction, formation of intermediates, rearrangement of
atoms, and the effect of different variables. There are certain factors
that affect the rate of reaction. They are the catalyst concentration of
reactants, and temperature. The prediction of the rate of reaction is
not possible and hence it has to be determined experimentally. The
mathematical representation of the rate of reaction is given by the
rate law.

7. Chemical kinetics and enzymes.
• Measurement of the rate of reaction of a chemical is done by
measuring either:
• Speed of the reactant consumed
• Speed of the product formed
• Collision

8. Chemical kinetics and enzymes.
• The chemical reactions occur only if the reactant molecules collide
with each other, this is called the collision theory of Chemical Kinetics.
• The collision states that In order to have a chemical reaction the
reactants must collide with adequate energy that is greater than the
activation energy (which is represented as Ea).

9. Chemical kinetics and enzymes.
• Rate of a Chemical Reaction
• Rate of a chemical reaction depends on the concentrations of
reactants or products and the time required to complete the chemical
change.
• Rate of a chemical reaction can be defined as the change in
concentration of a reactant or product in unit time.

10. Chemical kinetics and enzymes.
• Factors Influencing the Rate of Reaction
• There are certain factors that influence the rate of reaction, such as
increasing the fraction of molecules with energies greater than
activation energy Ea. The factors that influence the rate of a reaction
are,
• The Nature of the Reactants
• The Concentration of the Reactants
• The Temperature of the Reactants
• The Presence of a Catalyst

11. Optimization of an enzyme assay.
• To optimize an enzyme assay, keep in mind these five critical steps:
• Minimize background and promote higher specific signal
• There are a variety of methods to promote a strong signal while minimizing nonspecific binding and
background noise. Use a blocking buffer to block assay wells.
• This blocking of unoccupied space in the plate wells prevents nonspecific binding of sample and assay
components and reduces the overall background signal.
• Similarly, using the proper sample diluents will dilute the samples to read within the functional range,
minimize sample matrix effects, block nonspecific conjugate binding, and inhibit complement, all of which
reduce background noise and optimize signal.

12. Optimization of an enzyme assay.
• Improve precision by introducing enzyme co-factor
• Increase assay reproducibility: To increase the reproducibility of any assay, it is important to source reagents
from a consistent and reliable supplier.
• Look for established companies that offer strong customer support, an easy-to-use purchasing system, and
fast shipping options.

13. Optimization of an enzyme assay.
• Stabilize protein conjugates: Not only do conjugate stabilizer diluents inhibit nonspecific binding to reduce
background noise, but they also preserve enzymatic activity and protein conformation of enzyme conjugates.
• In addition, stabilizing conjugates enables you to store conjugated proteins and antibodies for future use,
prepare batches of diluted, ready-to-use conjugate aliquots, and reconstitute lyophilized conjugates while
preserving native protein configuration and activity.
• Increase shelf-life: Using dependable stabilizing and blocking buffers to stabilize proteins allow you to store
your prepared microtiter plates.
• Depending on the type of protein, properly prepared plates can be stored under proper conditions for
several months or even years if prepared using reliable reagents.
• Determine optimum temperation, pH, substrate concentration, enzyme concentration

14. chemical interactions: active site
• Only a certain region of the enzyme, called the active site, binds to the substrate.
• The active site is a groove or pocket formed by the folding pattern of the protein.
• This three-dimensional structure, together with the chemical and electrical properties of the amino acids
and cofactors within the active site, permits only a particular substrate to bind to the site, thus
determining the enzyme’s specificity.
• Reference to ionic, covalent, van de Waal and hydrophobic interaction.

15. chemical interactions: active site

16. hydrophobic interactions in biological
molecules
• Hydrophobic interactions describe the relations between water and hydrophobes (low water-soluble
molecules).
• Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not interact with
water molecules.
• The mixing of fat and water is a good example of this interaction.
• The common misconception is that water and fat doesn’t mix because the Van der Waals forces that are
acting upon both water and fat molecules are too weak.
• However, this is not the case. The behavior of a fat droplet in water has more to do with the enthalpy
and entropy of the reaction than its intermolecular forces.

17. hydrophobic interactions in biological
molecules
• Causes of Hydrophobic Interactions
• American chemist Walter Kauzmann discovered that nonpolar substances like fat molecules tend to
clump up together rather than distributing itself in a water medium, because this allow the fat molecules
to have minimal contact with water.

18. hydrophobic interactions in biological
molecules
• The image above indicates that when the hydrophobes come together, they will have less contact with
water.
• They interact with a total of 16 water molecules before they come together and only 10 atoms after they
interact.
• When a hydrophobe is dropped in an aqueous medium, hydrogen bonds between water molecules will
be broken to make room for the hydrophobe; however, water molecules do not react with hydrophobe.
• This is considered an endothermic reaction, because when bonds are broken heat is put into the system.
• Water molecules that are distorted by the presence of the hydrophobe will make new hydrogen bonds
and form an ice-like cage structure called a clathrate cage around the hydrophobe.

19. Strength of Hydrophobic Interactions
Hydrophobic interactions are relatively stronger than other weak intermolecular forces (i.e., Van der
Waals interactions or Hydrogen bonds). The strength of Hydrophobic Interactions depend on several
factors including (in order of strength of influence):
• Temperature: As temperature increases, the strength of hydrophobic interactions increases also. However,
at an extreme temperature, hydrophobic interactions will denature.
• Number of carbons on the hydrophobes: Molecules with the greatest number of carbons will have the
strongest hydrophobic interactions.
• The shape of the hydrophobes: Aliphatic organic molecules have stronger interactions than aromatic
compounds. Branches on a carbon chain will reduce the hydrophobic effect of that molecule and linear
carbon chain can produce the largest hydrophobic interaction. This is so because carbon branches produce
steric hindrance, so it is harder for two hydrophobes to have very close interactions with each other to
minimize their contact to water.

20. Hydrophobic Interactions
• Hydrophobic Interactions are important for the folding of proteins.
• This is important in keeping a protein stable and biologically active, because it allow to the protein to
decrease in surface are and reduce the undesirable interactions with water.
• Besides from proteins, there are many other biological substances that rely on hydrophobic interactions for
its survival and functions, like the phospholipid bilayer membranes in every cell of your body!